This study is part of a 16-year project to develop less invasive methods to diagnose pneumocystis pneumonia and to predict responses to therapy. Oral washes, induced sputum, and bronchalveolar lavage have been collected from patients with immunosuppressive diseases and respiratory syndromes. During this trial resulting studies have moved the field from a focus on tissue to a focus on respiratory secretions, especially secretions that can be obtained non-invasively. Oral washes have been collected prospectively from patients at San Francisco General Hospital who have HIV infection and possible pneumocystis pneumonia. Quantitative PCR had a high sensitivity and high specificity for identifying patients with pneumocystis penumonia, especially if a cut-off of 50 copies/uL were used. The initial phase of the study is completed. This PCR methodology has been adapted by the Microbiology Department at the NIH Clinical Center and is currently available as a routine test on respiratory specimens. Thus at present we have shifted our focus from diagnosis of PCP to better understanding the biology and epidemiology of Pneumocystis infection, although we remain interested in improved diagnostic methods. The study is still open for enrollment. An important goal of our studies is sequencing the Pneumocystis genome. In collaboration with investigators at Leidos and The Broad Institute, we have made progress in sequencing the mouse Pneumocystis genome (unpublished observations) but given the genetic differences between Pneumocystis species that infect different hosts, sequencing the P. jirovecii genome would provide important insights into its biology.